Multiple sequence alignment - TraesCS2D01G305300

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2D01G305300 chr2D 100.000 3035 0 0 1 3035 391112620 391115654 0.000000e+00 5605
1 TraesCS2D01G305300 chr2B 96.720 3049 57 14 14 3035 462300207 462303239 0.000000e+00 5036
2 TraesCS2D01G305300 chr2A 96.048 3062 80 13 1 3035 527700435 527703482 0.000000e+00 4946
3 TraesCS2D01G305300 chr3A 84.004 1119 124 28 1330 2436 57225902 57224827 0.000000e+00 1024
4 TraesCS2D01G305300 chr3A 85.465 172 21 4 2524 2692 57220352 57220182 3.110000e-40 176
5 TraesCS2D01G305300 chr3B 85.369 868 108 9 1342 2202 71327899 71327044 0.000000e+00 881
6 TraesCS2D01G305300 chr3B 86.180 521 41 14 2200 2716 71325243 71324750 4.450000e-148 534
7 TraesCS2D01G305300 chrUn 100.000 392 0 0 1219 1610 479687363 479687754 0.000000e+00 725


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G305300 chr2D 391112620 391115654 3034 False 5605.0 5605 100.0000 1 3035 1 chr2D.!!$F1 3034
1 TraesCS2D01G305300 chr2B 462300207 462303239 3032 False 5036.0 5036 96.7200 14 3035 1 chr2B.!!$F1 3021
2 TraesCS2D01G305300 chr2A 527700435 527703482 3047 False 4946.0 4946 96.0480 1 3035 1 chr2A.!!$F1 3034
3 TraesCS2D01G305300 chr3A 57224827 57225902 1075 True 1024.0 1024 84.0040 1330 2436 1 chr3A.!!$R2 1106
4 TraesCS2D01G305300 chr3B 71324750 71327899 3149 True 707.5 881 85.7745 1342 2716 2 chr3B.!!$R1 1374

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
393 398 1.555075 TCTCTTGGGCAGACATGGTAC 59.445 52.381 0.0 0.0 0.0 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2204 4045 1.39839 CCTGCATCGCTCCAAAACTAC 59.602 52.381 0.0 0.0 0.0 2.73 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 4.752101 GCACTTCGGCTATAAAGATCACAT 59.248 41.667 0.00 0.00 0.00 3.21
204 208 8.365399 TCGGTCTAATCAGCACAATAATTTAG 57.635 34.615 0.00 0.00 0.00 1.85
214 218 6.474427 CAGCACAATAATTTAGTGGCAAGATG 59.526 38.462 14.97 6.16 33.98 2.90
231 236 5.327091 CAAGATGAGGTTTCGCATTACTTG 58.673 41.667 0.00 0.00 33.59 3.16
248 253 2.634777 GCGCGTGCAACCTAAACA 59.365 55.556 17.66 0.00 42.15 2.83
252 257 1.659211 CGCGTGCAACCTAAACAAGAC 60.659 52.381 0.00 0.00 0.00 3.01
325 330 5.129980 TCTCAGATATGGATGGGCATATGTC 59.870 44.000 4.29 0.58 0.00 3.06
393 398 1.555075 TCTCTTGGGCAGACATGGTAC 59.445 52.381 0.00 0.00 0.00 3.34
430 435 1.741706 AGTAGCACACAAGCATCATGC 59.258 47.619 0.00 0.00 45.46 4.06
469 474 4.381411 AGTCTGCTACTGAAACTTTGGAC 58.619 43.478 0.00 0.00 36.93 4.02
505 510 7.424803 GTTATGCAATGTAACATATCCAAGCA 58.575 34.615 0.00 0.00 33.36 3.91
558 563 9.971922 CAAAAGGCTATCCTAAATTCCTAATTG 57.028 33.333 0.00 0.00 43.40 2.32
748 753 7.063544 GTGCTCCGAACATCAAATATATAGGAC 59.936 40.741 0.00 0.00 0.00 3.85
1084 1110 1.760405 ACCTTCCTCCTGGTTTCCAT 58.240 50.000 0.00 0.00 31.62 3.41
1217 1243 3.111484 TGGGAGCTGAATGGTATGTACA 58.889 45.455 0.00 0.00 0.00 2.90
1856 1893 6.183347 AGAATTAGAACCTTTGCTAGCACAT 58.817 36.000 19.17 1.44 0.00 3.21
2070 2107 9.502091 GAATATAAGTGTGTAATGGCCTAATGA 57.498 33.333 3.32 0.00 0.00 2.57
2922 4771 3.459232 TTGATGCGATACTGGAAGAGG 57.541 47.619 0.00 0.00 37.43 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 3.873910 AGCCGAAGTGCATACTATGTTT 58.126 40.909 0.00 0.00 35.69 2.83
12 13 7.090808 TCTTTATAGCCGAAGTGCATACTATG 58.909 38.462 0.00 0.00 35.69 2.23
43 44 0.179051 TGACCGCTGATATGCATGCA 60.179 50.000 25.04 25.04 0.00 3.96
140 141 7.100409 TCTTATTTGACGTGTGTTGGATATCA 58.900 34.615 4.83 0.00 0.00 2.15
204 208 0.169009 GCGAAACCTCATCTTGCCAC 59.831 55.000 0.00 0.00 0.00 5.01
231 236 0.996727 CTTGTTTAGGTTGCACGCGC 60.997 55.000 5.73 0.00 39.24 6.86
232 237 0.584396 TCTTGTTTAGGTTGCACGCG 59.416 50.000 3.53 3.53 0.00 6.01
234 239 3.684103 TTGTCTTGTTTAGGTTGCACG 57.316 42.857 0.00 0.00 0.00 5.34
235 240 5.348164 ACAATTGTCTTGTTTAGGTTGCAC 58.652 37.500 4.92 0.00 0.00 4.57
236 241 5.590530 ACAATTGTCTTGTTTAGGTTGCA 57.409 34.783 4.92 0.00 0.00 4.08
237 242 6.039616 TCAACAATTGTCTTGTTTAGGTTGC 58.960 36.000 12.39 0.00 40.30 4.17
239 244 8.695456 AGAATCAACAATTGTCTTGTTTAGGTT 58.305 29.630 12.39 0.00 40.30 3.50
240 245 8.137437 CAGAATCAACAATTGTCTTGTTTAGGT 58.863 33.333 12.39 0.00 40.30 3.08
241 246 8.137437 ACAGAATCAACAATTGTCTTGTTTAGG 58.863 33.333 12.39 7.08 40.30 2.69
242 247 9.173939 GACAGAATCAACAATTGTCTTGTTTAG 57.826 33.333 12.39 7.67 40.30 1.85
243 248 8.681806 TGACAGAATCAACAATTGTCTTGTTTA 58.318 29.630 12.39 0.00 40.30 2.01
244 249 7.546358 TGACAGAATCAACAATTGTCTTGTTT 58.454 30.769 12.39 8.72 40.30 2.83
245 250 7.099266 TGACAGAATCAACAATTGTCTTGTT 57.901 32.000 12.39 4.97 42.75 2.83
246 251 6.698008 TGACAGAATCAACAATTGTCTTGT 57.302 33.333 12.39 9.84 39.05 3.16
247 252 7.591165 AGATGACAGAATCAACAATTGTCTTG 58.409 34.615 12.39 7.76 41.93 3.02
248 253 7.446319 TGAGATGACAGAATCAACAATTGTCTT 59.554 33.333 12.39 6.15 41.93 3.01
252 257 6.150641 AGGTGAGATGACAGAATCAACAATTG 59.849 38.462 3.24 3.24 41.93 2.32
393 398 6.704493 TGTGCTACTTTAGGTACACTTCAAAG 59.296 38.462 0.00 1.02 35.50 2.77
430 435 6.457355 AGCAGACTCTTGCATCATAATCTAG 58.543 40.000 0.52 0.00 46.47 2.43
469 474 3.817084 ACATTGCATAACCATCTCATCCG 59.183 43.478 0.00 0.00 0.00 4.18
505 510 6.758886 GGATGTATTTGATCTTCGTTGACTCT 59.241 38.462 0.00 0.00 0.00 3.24
558 563 0.251341 ATGCTGGTTTGGGTGTCCTC 60.251 55.000 0.00 0.00 0.00 3.71
722 727 7.063544 GTCCTATATATTTGATGTTCGGAGCAC 59.936 40.741 0.00 0.00 0.00 4.40
748 753 6.764308 AATGTTGGATTTGGACAGAGTATG 57.236 37.500 0.00 0.00 0.00 2.39
778 786 2.026449 AGGGAGCTAATGATGCTATGCC 60.026 50.000 0.00 0.00 41.30 4.40
1008 1034 0.545646 AGAGGAAGATGGAAGGCTGC 59.454 55.000 0.00 0.00 0.00 5.25
1084 1110 0.606604 CTTCGTCGGAGGGGAAGAAA 59.393 55.000 7.31 0.00 38.72 2.52
1856 1893 3.069443 GGCACAAAACCCATTCTCTCAAA 59.931 43.478 0.00 0.00 0.00 2.69
2070 2107 6.534634 AGTAATTGCTAGTTGAAAGAGTGGT 58.465 36.000 0.00 0.00 0.00 4.16
2191 2228 6.627731 GCTCCAAAACTACTCCTAAGTCCTAC 60.628 46.154 0.00 0.00 36.92 3.18
2198 4034 4.755411 CATCGCTCCAAAACTACTCCTAA 58.245 43.478 0.00 0.00 0.00 2.69
2204 4045 1.398390 CCTGCATCGCTCCAAAACTAC 59.602 52.381 0.00 0.00 0.00 2.73
3006 4855 2.872245 ACCACACTCAACACTGATTTCG 59.128 45.455 0.00 0.00 0.00 3.46


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.